I modeled my protein on I TASSER and then tried to refine it on the modrefiner right on the desktop (the web version is unavailable). However, I get the following message: "PDB file can not be opened" (in this case, the protein I just modeled). Has anyone had a similar problem, and if so, any suggestions on how to resolve it? Both structures (the model and the template) are in PDB format. The command line I used was the same as indicated in the program's documentation.
./mcrefinement data_dir bin_dir ini_name ref_name ran_num
data_dir: data directory which contains ini_name. /
bin_dir : directory which contains all the library files. /
ini_name: model to be refined. /
ref_name: reference model which is also in data_dir. Only Ca atoms are used as restraints. The model doesn't require full-length and continuous backbone. /
str_val : strength value in [0,100]. Larger value makes the final model closer to the reference model. /
ran_num : random number in [0,1000000].